I won't try to go line for line and nitpick nor will I try to anticipate what may be coming, instead I'll just make a few very important points that just jump out at me upon reading this.
First, the idea that the 9/11 Commission report bolsters the contention that bin Laden basically adopted the ideas of Qutb. You are right that it states this directly, however I found it striking that it does not provide any example of bin Laden quoting Qutb -- I stil have yet to be provided with any. It doesn't even provide any source at all for this major claim, yet no doubt it could have found some, perhaps many articles claiming this, almost all written by people who are not specialists in Islam.
As you note that you don't entirely agree with their description of Qutb's thought, it must be stated directly that whoever wrote that paragraph or was the source of those ideas didn't understand Qutb in the least and it is hard to imagine had actually read Qutb. In no way did Qutb believe that "jahiliya could therefore triumph over Islam." The inevitability of the triumph of Islam is an article of faith for Islamists across the spectrum including Qutb. You may see this as another comparison to Marx, but this is the result of many direct statements in the Qur'an and Sunnah to this effect.
The idea that there is no middle ground in this struggle between God and Satan and all true believers must therefore take up arms in this fight sounds as much like George Bush as it does Qutb. In fact, as I've quoted to you previously Qutb neither took up arms himself and in fact directly counselled others not to take up arms.
I think the Khan argument does capture an element of Qutb's thought that was missing from your analysis, but I also agree it must be said in sincerity that there are huge differences between Qutb and Locke and in fact although Muqtedar Khan attempts to harness the name of Qutb to make an interesting intellectual point, in reality someone like Muqtedar Khan and someone like Sayyid Qutb if they lived at the same time and place would probably agree on almost nothing in terms of how to live the faith that they share in the public sphere. In fact, it is safe to say that Sayyid Qutb would see someone like Muqtedar Khan as a direct example of the danger to Muslims of adopting western ideologies over Islam.
One of the interesting things about people who believe in ideologies is the way they approach the practical events that occur in the world. Just as a true believer Marxist would claim that the atrocities of the Soviet Union were based on its own perversion of Marx and not Marx's teachings themselves, you and others who are firm believers in liberal democracy would claim that all of the atrocities of European/American civilization in terms of slavery, colonialism, racism, neo-colonialism, etc. are all exceptions which somehow result from the failure to live up to the ideals of Western civilization rather than being representative of the effects of that ideology. Similarly, you will probably see my attitude towards Islam. Now, I don't claim that all of these are morally equivalent. I have absolutely no interest in whether what Stalin did or what the Belgians did in the Congo is worse. All I'm saying is while to a certain extent it seems tantalizingly important to hold thinkers to task for the results of their thought, not just their intentions, it will never be fair or just unless one shows exactly how that thought must lead to those results and allows the person holding those thoughts (or someone on his/her behalf if he/she is dead) to argue that such was not what he/she was arguing for and attempt to prove it. This is what I have consistently attempted to do.